In the Content Manager, there’s an icon near the top right of the screen that lets you see individual items installed, not just complete packages. If you click that you’ll suddenly see hundreds if not thousands of specific things, not just a couple dozen. You can search though the list and see if you can remove specific buildings from WU X, but I admit I haven’t tried to do that - all I needed to uninstall personally was the Gaya-mada Catalina airport I referred to above.
If you can’t do what I suggest or if it’s just not possible, you could try reaching out to Drziewecki Design directly to ask if they can fix any overlap or morphing issues, or see if they can suggest a fix.